"In total 10 people were rescued and six people were found deceased", it said.
The bodies of the missing individuals were located Tuesday night, raising the death toll to six, the Coast Guard said.
Floatplanes have pontoons mounted under their fuselages so they can land on water.
The sightseers were all passengers from the cruise ship Royal Princess that was on a seven-day trip from Vancouver to Anchorage.
Searches are continuing for three other people missing after the crash on Monday.
"We are deeply saddened to report this news and our thoughts and prayers are with those who lost their lives and the families impacted by today's accident", Princess Cruises said in a statement. The ship is continuing to its next scheduled stop of Juneau.
The two aircraft came down in the sea off the southeastern coast of Alaska, around 25-30 miles (40-48km) northeast of the city of Ketchikan.
One aircraft, operated by Taquan Air, was flying a shore excursion sold through Princess Cruises.
Princess Cruises said rescue efforts were continuing for the unnamed Canadian and Australian, but Global Affairs Canada confirmed the Canadian was among those killed.
"The flight was returning from a Misty Fjords tour and carried ten guests from Royal Princess and a pilot".
The Coast Guard said it is "unaware" of why and how the planes collided.
The U.S. Coast Guard and search and rescue volunteers had been searching for the two missing people for over 12 hours and as recently as Tuesday evening, still held out hope they would find them alive.
"In a remote area such as this, give our limited resources, we rely on our partner agencies and appreciate the support good Samaritans have rendered to this point", he said.
"This is not the outcome we hoped for and extend our deepest sympathies during this very hard time".
Peter Knudson with the NTSB says the larger of the planes, the single-engine de Havilland Otter operated by Taquan Air, was initially travelling at an altitude of about 3,800 feet.
It's not yet known what caused the collision between the two planes, but National Transportation Safety Board investigators are on their way from Washington, D.C.to the crash site.
The family statement said he was adventurous, loved sailing, was a pilot himself and was very safety conscious.
The investigators will collect information from the survivors, the Federal Aviation Administration, other witnesses who might have been in the area, flight logs, training records and other sources, including the wrecked planes, Homendy said.
"A second float plane was also involved in an incident and was carrying four guests from Royal Princess on an independent tour", the company said, expressing their condolences to victims' families.